5jqr - Revision history

OCA at 19:02, 20 September 2023

OCA — Wed, 20 Sep 2023 19:02:41 GMT

←Older revision		Revision as of 19:02, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jqr' size='340' side='right'caption='[[5jqr]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='5jqr' size='340' side='right'caption='[[5jqr]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jqr]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Glycine_hispida~~ Glycine ~~hispida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JQR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JQR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jqr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JQR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.81Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5jpr\|5jpr]], [[2xif\|2xif]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">apx1~~, ~~GLYMA_U021900 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])~~<~~/td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jqr OCA], [https://pdbe.org/5jqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jqr RCSB], [https://www.ebi.ac.uk/pdbsum/5jqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jqr ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/L-ascorbate_peroxidase L-ascorbate peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.11 1.11.1.11]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jqr OCA], [~~http~~://pdbe.org/5jqr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jqr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jqr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jqr ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q43758_SOYBN Q43758_SOYBN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine ~~hispida]]~~	+	[[Category: Glycine max]]
-	~~[[Category: L-ascorbate peroxidase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kwon, H]]	+	[[Category: Kwon H]]
-	[[Category: Moody~~, P C.E~~]]	+	[[Category: Moody PCE]]
-	[[Category: Raven~~, E L]]~~	+	[[Category: Raven EL]]
-	~~[[Category: Compound ii]]~~	+
-	~~[[Category: Ferryl]]~~	+
-	~~[[Category: Heme peroxidase]]~~	+
-	~~[[Category: Intermediate]]~~	+
-	~~[[Category: Multicrystal]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:34, 17 June 2020

OCA — Wed, 17 Jun 2020 11:34:10 GMT

←Older revision		Revision as of 11:34, 17 June 2020
Line 1:		Line 1:

	==The Structure of Ascorbate Peroxidase Compound II formed by reaction with m-CPBA==		==The Structure of Ascorbate Peroxidase Compound II formed by reaction with m-CPBA==
-	<StructureSection load='5jqr' size='340' side='right' caption='[[5jqr]], [[Resolution\|resolution]] 1.81Å' scene=''>	+	<StructureSection load='5jqr' size='340' side='right'caption='[[5jqr]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jqr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JQR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JQR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jqr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JQR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JQR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jpr\|5jpr]], [[2xif\|2xif]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jpr\|5jpr]], [[2xif\|2xif]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apx1, GLYMA_U021900 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ascorbate_peroxidase L-ascorbate peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.11 1.11.1.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ascorbate_peroxidase L-ascorbate peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.11 1.11.1.11] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jqr OCA], [http://pdbe.org/5jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jqr RCSB], [http://www.ebi.ac.uk/pdbsum/5jqr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jqr ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jqr OCA], [http://pdbe.org/5jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jqr RCSB], [http://www.ebi.ac.uk/pdbsum/5jqr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jqr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5jqr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jqr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ascorbate peroxidase 3D structures\|Ascorbate peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Glycine hispida]]
	[[Category: L-ascorbate peroxidase]]		[[Category: L-ascorbate peroxidase]]
		+	[[Category: Large Structures]]
	[[Category: Kwon, H]]		[[Category: Kwon, H]]
	[[Category: Moody, P C.E]]		[[Category: Moody, P C.E]]

OCA at 21:25, 22 December 2016

OCA — Thu, 22 Dec 2016 21:25:25 GMT

←Older revision		Revision as of 21:25, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5jqr is ~~ON HOLD until Paper~~ Publication	+	==The Structure of Ascorbate Peroxidase Compound II formed by reaction with m-CPBA==
		+	<StructureSection load='5jqr' size='340' side='right' caption='[[5jqr]], [[Resolution\|resolution]] 1.81Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jqr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JQR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jpr\|5jpr]], [[2xif\|2xif]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ascorbate_peroxidase L-ascorbate peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.11 1.11.1.11] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jqr OCA], [http://pdbe.org/5jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jqr RCSB], [http://www.ebi.ac.uk/pdbsum/5jqr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jqr ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Catalytic heme enzymes carry out a wide range of oxidations in biology. They have in common a mechanism that requires formation of highly oxidized ferryl intermediates. It is these ferryl intermediates that provide the catalytic engine to drive the biological activity. Unravelling the nature of the ferryl species is of fundamental and widespread importance. The essential question is whether the ferryl is best described as a Fe(IV)=O or a Fe(IV)-OH species, but previous spectroscopic and X-ray crystallographic studies have not been able to unambiguously differentiate between the two species. Here we use a different approach. We report a neutron crystal structure of the ferryl intermediate in Compound II of a heme peroxidase; the structure allows the protonation states of the ferryl heme to be directly observed. This, together with pre-steady state kinetic analyses, electron paramagnetic resonance spectroscopy and single crystal X-ray fluorescence, identifies a Fe(IV)-OH species as the reactive intermediate. The structure establishes a precedent for the formation of Fe(IV)-OH in a peroxidase.

-	~~Authors~~:	+	Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme.,Kwon H, Basran J, Casadei CM, Fielding AJ, Schrader TE, Ostermann A, Devos JM, Aller P, Blakeley MP, Moody PC, Raven EL Nat Commun. 2016 Nov 29;7:13445. doi: 10.1038/ncomms13445. PMID:27897163<ref>PMID:27897163</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jqr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: L-ascorbate peroxidase]]
		+	[[Category: Kwon, H]]
		+	[[Category: Moody, P C.E]]
		+	[[Category: Raven, E L]]
		+	[[Category: Compound ii]]
		+	[[Category: Ferryl]]
		+	[[Category: Heme peroxidase]]
		+	[[Category: Intermediate]]
		+	[[Category: Multicrystal]]
		+	[[Category: Oxidoreductase]]

OCA at 13:42, 1 June 2016

OCA — Wed, 01 Jun 2016 13:42:33 GMT

←Older revision		Revision as of 13:42, 1 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jqr is ON HOLD	+	The entry 5jqr is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5jqr" [edit=sysop:move=sysop]

OCA — Sun, 15 May 2016 15:46:42 GMT

Protected "5jqr" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:46, 15 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jqr is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Sun, 15 May 2016 15:46:40 GMT

New page: '''Unreleased structure''' The entry 5jqr is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5jqr is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]